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5 Hypothyroid/Hashimoto’s Pitfalls to Avoid – My Story

My journey of getting an autoimmunity diagnosis is like many who have been diagnosed with autoimmune conditions.  Getting a correct diagnosis was a frustrating process that took over a decade and required advocating for my own health.  If I had understood more about the pitfalls I ran into, I might have been able to avoid years of suffering and preserved more of my thyroid gland from an autoimmune attack.  My hope is that by sharing my pitfalls, you, or someone you love can avoid them. 

Pitfalls At a Glance

  1. TPO & TgAb – Antibody testing informs whether hypothyroidism is due to autoimmunity (Hashimoto’s).  Having an accurate diagnosis creates an opportunity to make lifestyle interventions to address the autoimmune attack on the thyroid.
  2. Conventional Doctors do not believe that autoimmunity can be reversed, the concern is shutting symptoms off.  Functional Doctors do believe that autoimmunity can be reversed (not cured) by addressing underlying triggers.
  3. When hypothyroidism is due to Hashimoto’s – Dietary interventions can help with inflammation, leaky gut, and stopping the autoimmune attack on the thyroid (Myers, n.d.).
  4. Anti-inflammatory diets free from stressors (food sensitivities) are best for Hashimoto’s.  Do an elimination diet to find food sensitivities (Myers, n.d.).
  5. Test don’t guess.  Test for underlying imbalances instead of guessing at what they might be.


Pitfall #1 Not Understanding That the Most Common Forms of Thyroid Disease are Due to Autoimmunity (Myers, n.d.)

Hashimoto’s is the cause of an estimated 90% of hypothyroid cases (Kresser, 2022).  Had I known this when I received my hypothyroidism diagnosis, I would have asked for thyroid antibody tests (TPO & TgAb) to determine if the cause of my hypothyroidism was due to Hashimoto’s.  Having this information would have given me an opportunity to change lifestyle factors to address the autoimmune attack.  

Unfortunately, the attack on my thyroid continued for more than a decade because I didn’t have the right diagnosis.  I struggled with symptoms because my antibodies were not tested.  If you are hypothyroid, ask for antibody tests to be run.   Save yourself from the anger and frustration of a missed healing opportunity.  

  • Antibody tests are not the standard of care and are not run unless you have a functional doctor, or you ask for them. 

  • Thyroid medication only replaces the hormones your body is struggling to make – it does not stop the body from attacking the thyroid gland (autoimmunity).

  • Have you been told your thyroid labs are normal?   Normal values are based on a sick population and not on optimal levels (Kresser, 2018).  Here is a link to thyroid labs to ask for and understanding them.


Pitfall #2 – Not Understanding the Difference Between Treatment Options

Conventional doctors/endocrinologists do not test for autoimmunity when someone is hypothyroid because it makes no difference in how they treat hypothyroidism.  The conventional community does not believe that autoimmunity can be reversed and does not concern itself with finding underlying causes.  The goal of conventional care is the elimination of symptoms – shutting the fire alarm off while the house continues to burn down.

On the other hand, Functional physicians believe that while there is no cure for autoimmunity it can be reversed by addressing underlying causes with lifestyle and diet interventions (Hyman, n.d.).  Functional physicians look for what is causing the fire and address it; they stop the house from burning down.  I was not accurately diagnosed until I saw a Functional M.D. who tested my antibodies. 

  • Conventional medicine has its place and is necessary however, there is much room for improvement where chronic conditions are concerned. 

  • High cholesterol?  Have your thyroid checked (or thyroid meds adjusted).  High levels of total cholesterol, LDL, and triglycerides are common in people who are hypothyroid.  Proper thyroid medication can improve lipid profiles (Kesser, 2022).


Pitfall #3 Eating Gluten and Dairy 

The conventional world argues that there is no evidence to support cutting out gluten or dairy.  Arguments against cutting these foods out warn of restrictive diets being difficult to maintain, and the possibility of missing out on nutrients.  Both are valid concerns.  However, the decrease in inflammation and gut healing benefits outweigh those concerns for those who are dealing with Hashimoto’s.

Dr. Isabella Wentz recommends cutting both dairy and gluten out noting that Hashimoto’s patients that cut both out do much better (Wentz, 2021).  Furthermore, the elimination of gluten and dairy is the first pillar in Dr. Amy Myers 4R approach to healing the gut (Myers, n.d.). 

There are two reasons behind why the functional community supports cutting both gluten and dairy out – leaky gut and molecular mimicry.  Leaky gut is an inflammatory process and is associated with the development of autoimmune diseases (Paray et al., 2020).  It is a condition where the tight junctions in the lining of the intestines have become permeable.  This permeability allows microbes, toxins, and food particles that have not been properly broken down to pass through into the bloodstream (Myers, n.d.).  For those with Hashimoto’s, gluten is one of the main causes of leaky gut (Myers, n.d.).

Molecular mimicry happens when the protein sequences of molecules are similar. The body attacks itself because of mistaken identity, it does not recognize its own tissues (that is the description of an autoimmune attack).  

When a person with Hashimoto’s eats gluten, the immune system mounts an attack on the thyroid.  This happens because the body has a hard time distinguishing the difference between the protein sequence of gluten and the thyroid (molecular mimicry). Gluten gets flagged by the immune system as an invader when leaky gut is present; a condition that can be caused by gluten.  Furthermore, half of the people who are sensitive to gluten have cross reactivity with casein, the protein found in dairy.  (Myers, n.d.).  This means that for some of us diagnosed with Hashimoto’s, eating dairy can also cause the immune system to attack the thyroid.

I struggled with cutting both gluten and dairy out of my diet completely.  It was an arduous process.  Gluten is hidden in so many foods that were surprising to me…some salad dressings, caramel coloring, soy sauce, gum!  But…I feel so much better now that I don’t eat them anymore.  

Now I just deal with being ‘that girl’.  It sucks that being GF comes with a stigma – especially when not eating it is literally keeping my body from attacking itself.  At least it’s becoming more mainstream.  On that note, I’d recommend staying away from ‘mainstream’ GF foods not seen in nature…GF muffins, cookies, breads, etc.  Stick to naturally GF fare, meats, nuts, seeds, veggies, and fruits.  


Pitfall #4 Dietary Mistakes I Made

Pitfall…It is more difficult to get the protein and nutrients necessary when vegan.

After binge watching food documentaries on Netflix, I was convinced that being a whole foods vegan was the answer to my health problems.  Two years into my whole food vegan diet I had gained thirteen pounds. When I was diagnosed with Hashimoto’s, my functional doctor informed me that my vegan diet was inflammatory for me and might not be the best choice as I was deficient in many nutrients (B12, iron, selenium) despite supplementation.

Pitfall…I did not understand that the AIP diet is meant to be used temporarily as an elimination diet and should not be done long term. 

The point of AIP is having the most diverse diet possible.  The process is to temporarily remove foods that commonly cause inflammation and add them back in one at a time to identify food reactions.  I was still having symptoms on AIP, I stayed on the diet long term and failed to troubleshoot for underlying issues that were not food.  My excuse…resources on correct implementation were not available like they are now.  Here is a great resource for doing AIP correctly.

Pitfall…Being keto and hypothyroid puts major strain on the adrenals, and the reduced carb intake can lower thyroid hormone levels and can increase cortisol.  Use caution with keto if you have Hashimoto’s or if HPA axis dysfunction (adrenal fatigue) is an issue for you (Myers, n.d.).

Keto was the next diet I tried.  Initially this diet was helpful, but it led to hormonal issues for me due to user error. At the time I was mixing intermittent fasting with keto which is common but it was a mistake due to the state of my HPA axis dysfunction (adrenal fatigue). Additional errors I made were not syncing fasting with my cycle, not carb cycling, and not getting enough carbs for my thyroid to properly function.

  • Keto diet caution…Beware if you have the G allele of SNP rs5082 in the APOA2 gene, it interferes with saturated fat metabolism (Gardner, 2023).
  • Anti-inflammatory diets are best for Hashimoto’s…cut out alcohol, sugar, gluten, dairy, packaged and processed foods.
  • Whatever diet you choose to follow (keto, paleo, vegetarian, vegan), the best version is always the whole foods version.


Pitfall #5 Guessing

Pitfall…Not addressing underlying imbalances that keep antibodies high. 

Before I tested for underlying imbalances, every documentary or article I consumed would have me convinced that whatever they were talking about was my issue.  I would guess at what was causing my symptoms.  Then I’d be hopeful that the diet, supplement, or medication being promoted would be my cure-all. Guessing never worked.

Allergens, toxins, microbes, and dysbiosis (imbalance of good to bad bacteria in the gut) can all trigger symptoms and autoimmunity (Hyman, n.d.). Testing is the only way to know what is happening in your body.  I avoided testing for underlying issues because I didn’t prioritize spending money on testing. I could rationalize spending $40 for a supplement but it was difficult for me to pull the trigger on spending for testing.  

Finally, I had enough of not feeling well. I made a mental shift, and I prioritized spending money on uncovering my underlying issues.  When I finally tested – liver congestion, HPA axis dysfunction, hormonal issues, and gut issues were uncovered that I was able to treat. I could have saved myself some time, suffering, and money if I had tested sooner.

My hope is by sharing what I struggled with, you or a loved one can find a better way through the pitfalls I fell into along my hypothyroid journey.   

Article Sources

Bilal Ahmad Paray, M. F. (2020, December 21). Leaky Gut and Autoimmunity: An Intricate Balance in Individuals Health and the Diseased State. Retrieved from National Library of Medicine:

Gardner, D. A. (2023). GeneFood. Retrieved from APOA2:’G’%20allele%20of%20the,type%202%20diabetes%202%2C3.

Hyman, M. (n.d.). Is There A Cure For Autoimmune Disease. Retrieved from Mark Hyman:

Kresser, C. (2018, May 9). Five Thyroid Patterns That Won’t Show Up on Standard Lab Tests. Retrieved from Kresser Institute For Functional and Evolutionary Medicine:

Kresser, C. (2022, Oct 14). High Cholesterol? CVD Risk? It Might Be Your Thyroid. Retrieved from Chris Kesser, M.S.:

Lelwica Buttaccio OTR/L, J. (2023, April 21). The Symptoms, Causes, Diagnosis, and Treatment of Hashitoxicosis. Retrieved from verywell health:

Myers, A. (n.d.). Is Gluten to Blame for Your Hashimoto’s. Retrieved from Amy Myers M.D.:

Myers, A. (n.d.). What You Need to Know About Thyroid Disease. Retrieved from Amy Myers M.D.:

Wentz, I. (2021, Oct 29). Going Dairy Free to Reverse Hashimoto’s. Retrieved from Dr. Isabella Wentz PharmD: